SCEL
Basic information
Region (hg38): 13:77535673-77645263
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCEL gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 41 | 43 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 41 | 2 | 0 |
Variants in SCEL
This is a list of pathogenic ClinVar variants found in the SCEL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
13-77555907-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
13-77556598-A-T | not specified | Uncertain significance (Dec 14, 2023) | ||
13-77556608-C-T | not specified | Uncertain significance (May 11, 2022) | ||
13-77556623-C-G | not specified | Uncertain significance (Jan 25, 2023) | ||
13-77556625-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
13-77556675-G-C | not specified | Uncertain significance (Aug 04, 2021) | ||
13-77556703-G-A | not specified | Uncertain significance (Mar 21, 2023) | ||
13-77559817-G-A | Moyamoya angiopathy | Likely pathogenic (-) | ||
13-77559836-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
13-77559848-A-G | not specified | Uncertain significance (Aug 09, 2021) | ||
13-77563849-T-A | not specified | Uncertain significance (Dec 14, 2021) | ||
13-77563871-C-T | not specified | Uncertain significance (May 31, 2023) | ||
13-77567717-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
13-77567720-A-G | not specified | Uncertain significance (Feb 13, 2024) | ||
13-77569378-G-A | not specified | Uncertain significance (Feb 13, 2023) | ||
13-77572141-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
13-77572186-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
13-77572188-C-T | not specified | Uncertain significance (Jun 06, 2022) | ||
13-77589170-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
13-77591444-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
13-77591448-A-G | not specified | Uncertain significance (Aug 17, 2021) | ||
13-77597572-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
13-77599712-T-C | not specified | Uncertain significance (Jul 09, 2021) | ||
13-77602099-C-G | not specified | Uncertain significance (Jun 26, 2023) | ||
13-77602667-G-A | not specified | Uncertain significance (Jun 02, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCEL | protein_coding | protein_coding | ENST00000349847 | 32 | 109590 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.58e-21 | 0.128 | 125475 | 1 | 272 | 125748 | 0.00109 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.286 | 332 | 347 | 0.957 | 0.0000167 | 4592 |
Missense in Polyphen | 89 | 100.79 | 0.88305 | 1434 | ||
Synonymous | 1.46 | 93 | 113 | 0.825 | 0.00000570 | 1165 |
Loss of Function | 1.50 | 38 | 49.4 | 0.769 | 0.00000234 | 623 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0106 | 0.0106 |
Ashkenazi Jewish | 0.000214 | 0.000198 |
East Asian | 0.000195 | 0.000163 |
Finnish | 0.000417 | 0.000416 |
European (Non-Finnish) | 0.000374 | 0.000360 |
Middle Eastern | 0.000195 | 0.000163 |
South Asian | 0.000942 | 0.000915 |
Other | 0.00117 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: May function in the assembly or regulation of proteins in the cornified envelope. The LIM domain may be involved in homotypic or heterotypic associations and may function to localize sciellin to the cornified envelope.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.996
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 62.1
Haploinsufficiency Scores
- pHI
- 0.0815
- hipred
- N
- hipred_score
- 0.145
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.485
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Scel
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- epidermis development;response to mechanical stimulus;embryo development ending in birth or egg hatching;keratinocyte differentiation;positive regulation of canonical Wnt signaling pathway
- Cellular component
- cornified envelope;cytoplasm;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- protein binding;metal ion binding